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Fix number of threads used by MetaBAT2 program jgi_summarize_bam_contig_depths#57

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skrakau merged 3 commits intonf-core:devfrom
skrakau:fix_metabat_threads
Jun 29, 2020
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Fix number of threads used by MetaBAT2 program jgi_summarize_bam_contig_depths#57
skrakau merged 3 commits intonf-core:devfrom
skrakau:fix_metabat_threads

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@skrakau skrakau commented Jun 29, 2020

The jgi_summarize_bam_contig_depths program of MetaBAT2 uses by default all available threads (max. the number of samples).
Fixed the number of threads used with OpenMP OMP_NUM_THREADS environment variable.

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md

@skrakau skrakau requested a review from d4straub June 29, 2020 08:02
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Looks good to me

@skrakau skrakau merged commit 973f8d4 into nf-core:dev Jun 29, 2020
@skrakau skrakau deleted the fix_metabat_threads branch November 4, 2020 10:30
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2 participants